Implications of coral reef buildup for the controls on atmospheric CO2 since the Last Glacial Maximum

We examine the effect on atmospheric CO2 of the occurrence of increased shallow water carbonate deposition and regrowth of the terrestrial biosphere following the last glacial. We find that contrary to recent speculations that changes in terrestrial carbon storage were primarily responsible for the observed similar to20 ppmv late Holocene CO2 rise, a more likely explanation is coral reef buildup and other forms of shallow water carbonate deposition during this time. The importance of a responsive terrestrial carbon reservoir may instead be as a negative feedback restricting the rate of CO2 rise possible in the early stages of the deglacial transition. This separation in time of the primary impacts of regrowth of the terrestrial biosphere and increased shallow water carbonate deposition explains the occurrence of an early Holocene carbonate preservation event observed in deep-sea sediments. We demonstrate that their combined influence is also consistent with available proxy estimates of deep ocean carbonate ion concentration changes over the last 21 kyr. Accounting for the processes that act on the carbonate chemistry of the ocean as a whole then allows us to place strong constraints on the nature of the remaining processes that must be operating at the deglacial transition. By subtracting the net CO2 effect of coral reef buildup and terrestrial biosphere regrowth from recent high-resolution ice core data, we highlight two periods, from 17.0 to 13.8 kyr and 12.3 to 11.2 kyr BP characterized by sustained rapid rates of CO2 increase (> 12 ppmv kyr(-1)). Because these periods are coincident with Southern Hemisphere "deglaciation,'' we argue that changes in the biogeochemical properties of the Southern Ocean surface are the most likely cause

Oceans on the edge of anoxia

This is the author’s version of the work. It is posted here by permission of the AAAS for personal use, not for redistribution. The definitive version was published in Science vol 354 , pp. 1529-1530, December 23, 2016. DOI: 10.1126/science.aaj2321Environmental crises can tip the ocean into O2 depletio

A crucial sequence for transglutaminase type 2 extracellular trafficking in renal tubular epithelial cells lies in its N-terminal {beta}-sandwich domain

Transglutaminase type 2 (TG2) catalyzes the formation of an -( -glutamyl)-lysine isopeptide bond between adjacent peptides or proteins including those of the extracellular matrix (ECM). Elevated extracellular TG2 leads to accelerated ECM deposition and reduced clearance that underlie tissue scarring and fibrosis. The extracellular trafficking of TG2 is crucial to its role in ECM homeostasis; however, the mechanism by which TG2 escapes the cell is unknown as it has no signal leader peptide and therefore cannot be transported classically. Understanding TG2 transport may highlight novel mechanisms to interfere with the extracellular function of TG2 as isoform-specific TG2 inhibitors remain elusive. Mammalian expression vectors were constructed containing domain deletions of TG2. These were transfected into three kidney tubular epithelial cell lines, and TG2 export was assessed to identify critical domains. Point mutation was then used to highlight specific sequences within the domain required for TG2 export. The removal of -sandwich domain prevented all TG2 export. Mutations of Asp94 and Asp97 within the N-terminal -sandwich domain were identified as crucial for TG2 externalization. These form part of a previously identified fibronectin binding domain (88WTATVVDQQDCTLSLQLTT106). However, siRNA knockdown of fibronectin failed to affect TG2 export. The sequence 88WTATVVDQQDCTLSLQLTT106 within the -sandwich domain of TG2 is critical to its export in tubular epithelial cell lines. The extracellular trafficking of TG2 is independent of fibronectin

Ocean de-oxygenation, the global phosphorus cycle, and the possibility of human-caused large-scale ocean anoxia

The major biogeochemical cycles that keep the present-day Earth habitable are linked by a network of feedbacks, which has led to a broadly stable chemical composition of the oceans and atmosphere over hundreds of millions of years. This includes the processes that control both the atmospheric and oceanic concentrations of oxygen. However, one notable exception to the generally well-behaved dynamics of this system is the propensity for episodes of ocean anoxia to occur and to persist for 105–106 years, these ocean anoxic events (OAEs) being particularly associated with warm ‘greenhouse’ climates. A powerful mechanism responsible for past OAEs was an increase in phosphorus supply to the oceans, leading to higher ocean productivity and oxygen demand in subsurface water. This can be amplified by positive feedbacks on the nutrient content of the ocean, with low oxygen promoting further release of phosphorus from ocean sediments, leading to a potentially self-sustaining condition of deoxygenation. We use a simple model for phosphorus in the ocean to explore this feedback, and to evaluate the potential for humans to bring on global-scale anoxia by enhancing P supply to the oceans. While this is not an immediate global change concern, it is a future possibility on millennial and longer time scales, when considering both phosphate rock mining and increased chemical weathering due to climate change. Ocean deoxygenation, once begun, may be self-sustaining and eventually could result in long-lasting and unpleasant consequences for the Earth's biosphere

The capacity of people with a ‘mental disability’ to make a health care decision

Background. Based on the developing clinical and legal literature, and using the framework adopted in draft legislation, capacity to make a valid decision about a clinically required blood test was investigated in three groups of people with a ‘mental disability’ (i.e. mental illness (chronic schizophrenia), ‘learning disability’ (‘mental retardation’, or intellectual or developmental disability), or, dementia) and a fourth, comparison group. Methods. The three ‘mental disability’ groups (N = 20 in the ‘learning disability’ group, N = 21 in each of the other two groups) were recruited through the relevant local clinical services; and through a phlebotomy clinic for the ‘general population’ comparison group (N = 20). The decision-making task was progressively simplified by presenting the relevant information as separate elements and modifying the assessment of capacity so that responding became gradually less dependent on expressive verbal ability. Results. Compared with the ‘general population’ group, capacity to make the particular decision was significantly more impaired in the ‘learning disability’ and ‘dementia’ groups. Importantly, however, it was not more impaired among the ‘mental illness’ group. All the groups benefited as the decision-making task was simplified, but at different stages. In each of the ‘mental disability’ groups, one participant benefited only when responding did not require any expensive verbal ability. Conclusions. Consistent with current views, capacity reflected an interaction between the decision-maker and the demands of the decision-making task. The findings have implications for the way in which decisions about health care interventions are sought from people with a ‘mental disability’. The methodology may be extended to assess capacity to make other legally-significant decisions.published_or_final_versio

Transcription enhancement of a digitised multi-lingual pamphlet collection: a case study and guide for similar projects

UCL Library Services holds an extensive collection of over 9,000 Jewish pamphlets, many of these extremely rare. Over the past five years, UCL has embarked on a project to widen access to this collection through an extensive programme of cataloguing, conservation and digitisation. With the cataloguing complete and the most fragile items conserved, the focus is now on making these texts available to global audiences via UCL Digital Collections website. The pamphlets were ranked for rarity, significance and fragility and the highest-scoring selected for digitisation. Unique identifiers allocated at the point of cataloguing were used to track individual pamphlets through the stages of the project. This guide details the text-enhancement methods used, highlighting particular issues relating to Hebrew scripts and early-printed texts. Initial attempts to enable images of these pamphlets to be searched digitally relied on the Optical Character Recognition (OCR) embedded within the software used to create the PDF files. Whilst satisfactory for texts chiefly in Roman script, it provided no reliable means to search the extensive corpus of texts in Hebrew. Generous advice offered by the National Library of Israel led to our adoption of ABBYY FineReader software as a means of enhancing the transcriptions embedded within the PDF files. Following image capture, JPEG files were used to create multi-page PDF files of each pamphlet. Pre-processing in ABBYY FineReader consisted of: setting the language and colour mode; detecting page orientation; selecting and refining areas of the text to be read; reading the text to produce a transcription. The resultant files were stored in folders according to language of text. The software highlighted spelling errors and doubtful readings. A verification tool allowed transcribers to correct these as required. However, some erroneous or doubtful readings were nevertheless genuine words and not highlighted; it was therefore essential to proofread the text, particularly for early-printed scripts. Transcribers maintained logs of common errors; additionally, problems with Hebrew vocalisations, cursive and Gothic scripts were noted. During initial quality checks of the transcriptions, many text searches were unsuccessful due to previously unidentified spacings occurring within words. This was generally linked to the font size being too small. Maintaining logs of font sizes used led to the adoption of a minimum of Arial 8 or Times New Roman 10 in transcribed text. The methodology was revised to include the preliminary quality-checking of one page. We concluded that it was difficult to develop a standardised procedure applicable to all texts given the variance in language, script and typography. However, we concluded that the font Arial gave the most successful accuracy ratings for Hebrew script, minimum text size 17, minimum title size 25. ABBYY file preparation took a minimum of 1.5 hours per pamphlet; transcription correction took an average of 10.4 minutes per page; the final quality check took 30 minutes per pamphlet. On average, the work on each pamphlet took a minimum of 6 hours to complete. As a result of the project, average accuracy ratings improved from 60% to 89%, the greatest improvement being for pre-1800 and Hebrew script publications. We are therefore inclined to focus future transcription-enhancement activity on these types of publication for the remainder of our Jewish Pamphlet Collections

The potential impact of Brexit on the energy, water and food nexus in the UK: A fuzzy cognitive mapping approach

© 2017 The Authors. Energy is one of the cornerstones essential for human life, along with other services such as water and food. Understanding how the different services in the energy-water-food (EWF) nexus interact and are perceived by different actors is key to achieving sustainability. In this paper, we derive a model of the EWF nexus using fuzzy cognitive mapping (FCM). Data were collected in a two-step approach from workshops with researchers and stakeholders involved in the three focal sectors. Four FCMs were developed; one for each of the EWF sectors, and one for the interactions that create the nexus between EWF. The FCM represents the combined views of the groups who participated in the workshops, the importance and limitations of which is discussed. To demonstrate its effectiveness, the aggregated FCM was applied to predict the impacts on the EWF nexus of four scenarios under which the United Kingdom would depart from the European Union (i.e. Brexit). The FCM indicated that energy-related concepts had the largest influence on the EWF nexus and that EWF demand will decrease most under a 'hard-Brexit' scenario. The demand for energy was shown to decline relatively less than other services and was strongly associated with gross domestic product (GDP), whereas UK population size had a stronger effect on water and food demand. Overall, we found a threefold change across all concepts in scenarios without freedom of movement, contribution to the EU budget, and increased policy devolution to the UK

Meridional Overturning Circulation in a multi-basin model. Part II: Sensitivity to diffusivity and wind in warm and cool climates

This is the final version. Available from the American Meteorological Society via the DOI in this record. The response of the meridional overturning circulation (MOC) to changes in Southern Ocean (SO) zonal wind forcing and Pacific basin vertical diffusivity is investigated under varying buoyancy forcings, corresponding to ‘warm’, ‘present-day’ and ‘cold’ states, in a two-basin general circulation model connected by a southern circumpolar channel. We find that the Atlantic MOC (AMOC) strengthens with increased SO wind stress or diffusivity in the model Pacific, under all buoyancy forcings. The sensitivity of the AMOC to wind stress increases as the buoyancy forcing is varied from a warm to a present-day or cold state, whereas it is most sensitive to the Pacific diffusivity in a present-day or warm state. Similarly, the AMOC is more sensitive to buoyancy forcing over the Southern Ocean under reduced wind stress or enhanced Pacific diffusivity. These results arise because of the increased importance of the Pacific pathway in the warmer climates, giving an increased linkage between the basins and so the opportunity for the diffusivity in the Pacific to affect the overturning in the Atlantic. In cooler states, such as in glacial climates, the two basins are largely decoupled and the wind strength over the SO is the primary determinant of the AMOC strength. Both wind- and diffusively-driven upwelling sustain the AMOC in the warmer (present-day) state. Changes in SO wind stress alone do not shoal the AMOC to resemble that observed at the last glacial maximum; changes in the buoyancy forcing are also needed to decouple the two basins.Natural Environment Research Council (NERC)Royal Societ

A novel cell culture model for studying differentiation and apoptosis in the mouse mammary gland.

BACKGROUND: This paper describes the derivation and characterization of a novel, conditionally immortal mammary epithelial cell line named KIM-2. These cells were derived from mid-pregnant mammary glands of a mouse harbouring one to two copies of a transgene comprised of the ovine beta-lactoglobulin milk protein gene promoter, driving expression of a temperature-sensitive variant of simian virus-40 (SV40) large T antigen (T-Ag). RESULTS: KIM-2 cells have a characteristic luminal epithelial cell morphology and a stable, nontransformed phenotype at the semipermissive temperature of 37 degrees C. In contrast, at the permissive temperature of 33 degrees C the cells have an elongated spindle-like morphology and become transformed after prolonged culture. Differentiation of KIM-2 cells at 37 degrees C, in response to lactogenic hormones, results in the formation of polarized dome-like structures with tight junctions. This is accompanied by expression of the milk protein genes that encode beta-casein and whey acidic protein (WAP), and activation of the prolactin signalling molecule, signal transducer and activator of transcription (STAT)5. Fully differentiated KIM-2 cultures at 37 degrees C become dependent on lactogenic hormones for survival and undergo extensive apoptosis upon hormone withdrawal, as indicated by nuclear morphology and flow cytometric analysis. KIM-2 cells can be genetically modified by stable transfection and clonal lines isolated that retain the characteristics of untransfected cells. CONCLUSION: KIM-2 cells are a valuable addition, therefore, to currently available lines of mammary epithelial cells. Their capacity for extensive differentiation in the absence of exogenously added basement membrane, and ability to undergo apoptosis in response to physiological signals will provide an invaluable model system for the study of signal transduction pathways and transcriptional regulatory mechanisms that control differentiation and involution in the mammary gland

Long Term Planetary Habitability and the Carbonate-Silicate Cycle

The potential habitability of an exoplanet is traditionally assessed by determining whether its orbit falls within the circumstellar “habitable zone” of its star, defined as the distance at which water could be liquid on the surface of a planet (Kopparapu et al.,2013). Traditionally, these limits are determined by radiative-convective climate models, which are used to predict surface temperatures at user-specified levels of greenhouse gases. This approach ignores the vital question of the (bio)geochemical plausibility of the proposed chemical abundances. Carbon dioxide is the most important greenhouse gas in Earth's atmosphere in terms of regulating planetary temperature, with the long-term concentration controlled by the balance between volcanic outgassing and the sequestration of CO2 via chemical weathering and sedimentation, as modulated by ocean chemistry, circulation, and biological (microbial) productivity. We developed a model that incorporates key aspects of Earth's short- and long-term biogeochemical carbon cycle to explore the potential changes in the CO2 greenhouse due to variance in planet size and stellar insolation. We find that proposed changes in global topography, tectonics, and the hydrological cycle on larger planets result in proportionally greater surface temperatures for a given incident flux. For planets between 0.5 and 2 R⊕, the effect of these changes results in average global surface temperature deviations of up to 20 K, which suggests that these relationships must be considered in future studies of planetary habitability